Add segment information for each atom (#10)

* add segment information * add segment information --------- Co-authored-by: pegerto-fernandez-ck <[email protected]>
pegerto · Nov 21, 2023 · 7a576a7 · 7a576a7
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,9 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
 
+## Next
+ * [New] Include segmentid for freesasa calculation.
+
 ## 0.1.2 
  * [Fix] Clean area calculation
 

diff --git a/mdakit_sasa/analysis/sasaanalysis.py b/mdakit_sasa/analysis/sasaanalysis.py
@@ -78,10 +78,10 @@ def _single_frame(self):
         """Calculate data from a single frame of trajectory"""
 
         structure = freesasa.Structure()  
-        # FreeSasa structure accepts PDBS if not available requires to reconstruct the structure using `adAtom`
+        # FreeSasa structure accepts PDBS if not available requires to reconstruct the structure using `addAtom`
         for a in self.atomgroup:
             x,y,z = a.position            
-            structure.addAtom(a.name, a.resname, a.resnum.item(), "", x, y, z)
+            structure.addAtom(a.name, a.resname, a.resnum.item(), a.segid, x, y, z)
 
         # Define 1 cpu for windows avoid freesasa code to calculate it.
         parametes =  freesasa.Parameters()

diff --git a/mdakit_sasa/tests/analysis/test_sasaanalysis.py b/mdakit_sasa/tests/analysis/test_sasaanalysis.py
@@ -5,7 +5,7 @@
 
 from mdakit_sasa.analysis.sasaanalysis import SASAAnalysis
 from mdakit_sasa.tests.utils import make_Universe
-from MDAnalysis.core.topologyattrs import Atomnames, Resnames, Resids, Resnums
+from MDAnalysis.core.topologyattrs import Atomnames, Resnames, Resids, Resnums, Segids
 
 class TestSASAAnalysis:
 
@@ -24,6 +24,7 @@ def universe(self):
         u.add_TopologyAttr(Resnames(["GLY"] * len(u.residues)))
         u.add_TopologyAttr(Resids(list(range(0, len(u.residues)))))
         u.add_TopologyAttr(Resnums(list(range(0, len(u.residues)))))
+        u.add_TopologyAttr(Segids(["A"] * len(u.segments)))
         return u
 
     @pytest.fixture